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Prof. Dr. Ana Abecasis
Global Health and Tropical Medicine, Universidade Nova de Lisboa, Lisbon, Portugal

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0 Evolution
0 Molecular Epidemiology
0 SARS-CoV2
0 Transmission of infectious diseases
0 Development of hiv resistance to antiretrovirals

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Journal article
Published: 02 July 2021 in Pathogens
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To control the Human Immunodeficiency Virus (HIV) pandemic, the World Health Organization (WHO) set the 90-90-90 target to be reached by 2020. One major threat to those goals is late presentation, which is defined as an individual presenting a TCD4+ count lower than 350 cells/mm3 or an AIDS-defining event. The present study aims to identify determinants of late presentation in Europe based on the EuResist database with HIV-1 infected patients followed-up between 1981 and 2019. Our study includes clinical and socio-demographic information from 89851 HIV-1 infected patients. Statistical analysis was performed using RStudio and SPSS and a Bayesian network was constructed with the WEKA software to analyze the association between all variables. Among 89,851 HIV-1 infected patients included in the analysis, the median age was 33 (IQR: 27.0–41.0) years and 74.4% were males. Of those, 28,889 patients (50.4%) were late presenters. Older patients (>56), heterosexuals, patients originated from Africa and patients presenting with log VL >4.1 had a higher probability of being late presenters (p< 0.001). Bayesian networks indicated VL, mode of transmission, age and recentness of infection as variables that were directly associated with LP. This study highlights the major determinants associated with late presentation in Europe. This study helps to direct prevention measures for this population.

ACS Style

Mafalda Miranda; Marta Pingarilho; Victor Pimentel; Maria Martins; Anne-Mieke Vandamme; Marina Bobkova; Michael Böhm; Carole Seguin-Devaux; Roger Paredes; Rafael Rubio; Maurizio Zazzi; Francesca Incardona; Ana Abecasis. Determinants of HIV-1 Late Presentation in Patients Followed in Europe. Pathogens 2021, 10, 835 .

AMA Style

Mafalda Miranda, Marta Pingarilho, Victor Pimentel, Maria Martins, Anne-Mieke Vandamme, Marina Bobkova, Michael Böhm, Carole Seguin-Devaux, Roger Paredes, Rafael Rubio, Maurizio Zazzi, Francesca Incardona, Ana Abecasis. Determinants of HIV-1 Late Presentation in Patients Followed in Europe. Pathogens. 2021; 10 (7):835.

Chicago/Turabian Style

Mafalda Miranda; Marta Pingarilho; Victor Pimentel; Maria Martins; Anne-Mieke Vandamme; Marina Bobkova; Michael Böhm; Carole Seguin-Devaux; Roger Paredes; Rafael Rubio; Maurizio Zazzi; Francesca Incardona; Ana Abecasis. 2021. "Determinants of HIV-1 Late Presentation in Patients Followed in Europe." Pathogens 10, no. 7: 835.

Journal article
Published: 16 February 2021 in AIDS Research and Human Retroviruses
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Background: Undiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters for HIV care may help to identify characteristics of such patients. Objective: The present study aims to identify factors associated with late presentation (LP) and late presentation with advanced disease (LPAD) based on a population of patients followed in a Portuguese hospital between 1984 and 2017. Methods: Sociodemographic and clinical data from infected patients with HIV-1 aged 18 years and older, followed in Egas Moniz Hospital, in Portugal were collected. Results: Of the 907 patients included in this study, 68.7% were males and the median age was 37 years (IQR 30-47). 459 patients (50.6%) were LP and, of these, 284 patients (61.9%) were LPAD. The LP population mostly originated from Portugal and Sub-Saharan Africa (64.4% and 28.8%; p=0.004) and the HIV exposure category mainly heterosexuals and MSM (57.0% and 24.9%; p<0.001). The stage of disease and viral load at diagnosis were significantly associated with both LP and LPAD (p<0.001). Factors associated with LP in the logistic regression included age at diagnosis lower than 30y (aOR 0.34; 0.17-0.68; p=0.002) and origin from Sub-Saharan Africa (aOR 2.24; 1.44-3.50; p<0.001). Conclusion: Late presentation is a major obstacle to halt the HIV epidemic. In this population, the majority of newly diagnosed HIV-infected individuals were late presenters. Our results characterize vulnerable populations that should be frequently tested for HIV. Keywords: HIV-1 infection, Late presentation, Late presentation with advanced disease

ACS Style

Ana Cláudia Miranda; Miss Mafalda Miranda; Marta Pingarilho; Victor Pimentel; João Torres; Susana Peres; Teresa Baptista Alberto; Perpetua Gomes; Ana B. Abecasis; Kamal Mansinho. Determinants of HIV-1 Late Presentation in a Cohort of Portuguese HIV-1 Patients. AIDS Research and Human Retroviruses 2021, 1 .

AMA Style

Ana Cláudia Miranda, Miss Mafalda Miranda, Marta Pingarilho, Victor Pimentel, João Torres, Susana Peres, Teresa Baptista Alberto, Perpetua Gomes, Ana B. Abecasis, Kamal Mansinho. Determinants of HIV-1 Late Presentation in a Cohort of Portuguese HIV-1 Patients. AIDS Research and Human Retroviruses. 2021; ():1.

Chicago/Turabian Style

Ana Cláudia Miranda; Miss Mafalda Miranda; Marta Pingarilho; Victor Pimentel; João Torres; Susana Peres; Teresa Baptista Alberto; Perpetua Gomes; Ana B. Abecasis; Kamal Mansinho. 2021. "Determinants of HIV-1 Late Presentation in a Cohort of Portuguese HIV-1 Patients." AIDS Research and Human Retroviruses , no. : 1.

Journal article
Published: 30 October 2020 in Viruses
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Introduction: Treatment for All recommendations have allowed access to antiretroviral (ARV) treatment for an increasing number of patients. This minimizes the transmission of infection but can potentiate the risk of transmitted (TDR) and acquired drug resistance (ADR). Objective: To study the trends of TDR and ADR in patients followed up in Portuguese hospitals between 2001 and 2017. Methods: In total, 11,911 patients of the Portuguese REGA database were included. TDR was defined as the presence of one or more surveillance drug resistance mutation according to the WHO surveillance list. Genotypic resistance to ARV was evaluated with Stanford HIVdb v7.0. Patterns of TDR, ADR and the prevalence of mutations over time were analyzed using logistic regression. Results and Discussion: The prevalence of TDR increased from 7.9% in 2003 to 13.1% in 2017 (p < 0.001). This was due to a significant increase in both resistance to nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleotide reverse transcriptase inhibitors (NNRTIs), from 5.6% to 6.7% (p = 0.002) and 2.9% to 8.9% (p < 0.001), respectively. TDR was associated with infection with subtype B, and with lower viral load levels (p < 0.05). The prevalence of ADR declined from 86.6% in 2001 to 51.0% in 2017 (p < 0.001), caused by decreasing drug resistance to all antiretroviral (ARV) classes (p < 0.001). Conclusions: While ADR has been decreasing since 2001, TDR has been increasing, reaching a value of 13.1% by the end of 2017. It is urgently necessary to develop public health programs to monitor the levels and patterns of TDR in newly diagnosed patients.

ACS Style

Marta Pingarilho; Victor Pimentel; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea Pineda-Pena; Pieter Libin; Kristof Theys; M. Rosário O. Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis; on behalf of the Portuguese HIV-1 Resistance Study Group. Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations. Viruses 2020, 12, 1238 .

AMA Style

Marta Pingarilho, Victor Pimentel, Isabel Diogo, Sandra Fernandes, Mafalda Miranda, Andrea Pineda-Pena, Pieter Libin, Kristof Theys, M. Rosário O. Martins, Anne-Mieke Vandamme, Ricardo Camacho, Perpétua Gomes, Ana Abecasis, on behalf of the Portuguese HIV-1 Resistance Study Group. Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations. Viruses. 2020; 12 (11):1238.

Chicago/Turabian Style

Marta Pingarilho; Victor Pimentel; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea Pineda-Pena; Pieter Libin; Kristof Theys; M. Rosário O. Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis; on behalf of the Portuguese HIV-1 Resistance Study Group. 2020. "Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations." Viruses 12, no. 11: 1238.

Other
Published: 20 June 2020
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BackgroundUndiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters for HIV care may help to identify characteristics of such patients.ObjectiveThe present study aims to identify factors associated with late presentation (LP) and late presentation with advanced disease (LPAD) based on a population of patients followed in a Portuguese hospital between 1984 and 2017.MethodsSociodemographic and clinical data from infected patients with HIV-1 aged 18 years and older, followed in Egas Moniz Hospital, in Portugal were collected.ResultsOf the 907 patients included in this study, 68.7% were males and the median age was 37 years (IQR 30-47). 459 patients (50.6%) were LP and, of these, 284 patients (61.9%) were LPAD. The LP population mostly originated from Portugal and Sub-Saharan Africa (64.4% and 28.8%; p=0.004) and the HIV exposure category mainly heterosexuals and MSM (57.0% and 24.9%; ppp=0.002) and origin from Sub-Saharan Africa (aOR 2.24; 1.44-3.50; pConclusionLate presentation is a major obstacle to halt the HIV epidemic. In this population, the majority of newly diagnosed HIV-infected individuals were late presenters. Our results characterize vulnerable populations that should be frequently tested for HIV.

ACS Style

Ana Cláudia Miranda; Mafalda Miranda; Marta Pingarilho; Victor Pimentel; João Torres; Susana Peres; Teresa Baptista Alberto; Perpetua Gomes; Ana Abecasis; Kamal Mansinho. Determinants of HIV-1 late presentation in a cohort of Portuguese HIV-1 patients. 2020, 1 .

AMA Style

Ana Cláudia Miranda, Mafalda Miranda, Marta Pingarilho, Victor Pimentel, João Torres, Susana Peres, Teresa Baptista Alberto, Perpetua Gomes, Ana Abecasis, Kamal Mansinho. Determinants of HIV-1 late presentation in a cohort of Portuguese HIV-1 patients. . 2020; ():1.

Chicago/Turabian Style

Ana Cláudia Miranda; Mafalda Miranda; Marta Pingarilho; Victor Pimentel; João Torres; Susana Peres; Teresa Baptista Alberto; Perpetua Gomes; Ana Abecasis; Kamal Mansinho. 2020. "Determinants of HIV-1 late presentation in a cohort of Portuguese HIV-1 patients." , no. : 1.

Letter
Published: 07 May 2020 in Proceedings of the National Academy of Sciences
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ACS Style

Carla Mavian; Sergei Kosakovsky Pond; Simone Marini; Brittany Rife Magalis; Anne-Mieke Vandamme; Simon Dellicour; Samuel V. Scarpino; Charlotte Houldcroft; Julian Villabona-Arenas; Taylor K. Paisie; Nídia S. Trovão; Christina Boucher; Yun Zhang; Richard H. Scheuermann; Olivier Gascuel; Tommy Tsan-Yuk Lam; Marc A. Suchard; Ana Abecasis; Eduan Wilkinson; Tulio de Oliveira; Ana I. Bento; Heiko A. Schmidt; Darren Martin; James Hadfield; Nuno Rodrigues Faria; Nathan D. Grubaugh; Richard A. Neher; Guy Baele; Philippe Lemey; Tanja Stadler; Jan Albert; Keith A. Crandall; Thomas Leitner; Alexandros Stamatakis; Mattia Prosperi; Marco Salemi. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences 2020, 117, 12522 -12523.

AMA Style

Carla Mavian, Sergei Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne-Mieke Vandamme, Simon Dellicour, Samuel V. Scarpino, Charlotte Houldcroft, Julian Villabona-Arenas, Taylor K. Paisie, Nídia S. Trovão, Christina Boucher, Yun Zhang, Richard H. Scheuermann, Olivier Gascuel, Tommy Tsan-Yuk Lam, Marc A. Suchard, Ana Abecasis, Eduan Wilkinson, Tulio de Oliveira, Ana I. Bento, Heiko A. Schmidt, Darren Martin, James Hadfield, Nuno Rodrigues Faria, Nathan D. Grubaugh, Richard A. Neher, Guy Baele, Philippe Lemey, Tanja Stadler, Jan Albert, Keith A. Crandall, Thomas Leitner, Alexandros Stamatakis, Mattia Prosperi, Marco Salemi. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences. 2020; 117 (23):12522-12523.

Chicago/Turabian Style

Carla Mavian; Sergei Kosakovsky Pond; Simone Marini; Brittany Rife Magalis; Anne-Mieke Vandamme; Simon Dellicour; Samuel V. Scarpino; Charlotte Houldcroft; Julian Villabona-Arenas; Taylor K. Paisie; Nídia S. Trovão; Christina Boucher; Yun Zhang; Richard H. Scheuermann; Olivier Gascuel; Tommy Tsan-Yuk Lam; Marc A. Suchard; Ana Abecasis; Eduan Wilkinson; Tulio de Oliveira; Ana I. Bento; Heiko A. Schmidt; Darren Martin; James Hadfield; Nuno Rodrigues Faria; Nathan D. Grubaugh; Richard A. Neher; Guy Baele; Philippe Lemey; Tanja Stadler; Jan Albert; Keith A. Crandall; Thomas Leitner; Alexandros Stamatakis; Mattia Prosperi; Marco Salemi. 2020. "Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable." Proceedings of the National Academy of Sciences 117, no. 23: 12522-12523.

Other
Published: 20 March 2020
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Background Treatment for all recommendations has allowed access to antiretroviral (ARV) treatment to an increasing number of patients. This minimizes transmission of infection but can potentiate the risk for development of transmitted drug resistance (TDR) and acquired drug resistance (ADR). Objective To study the trends of TDR and ADR in patients followed in Portuguese hospitals between 2001 and 2017. Method 11911 patients of the Portuguese REGA database were included. TDR was defined as the presence of one or more surveillance drug resistance mutations according to the WHO surveillance list. Phenotypic resistance to ARV was evaluated with Standford HIVdb v7.0. Patterns of TDR, ADR and prevalence of mutations over time were analysed with logistic regression. Results The prevalence of TDR increased from 7.9% in 2003 to 13.1% in 2017 (pfor-trendfor-trend=0.002) and 2.9% to 8.9% (pfor-trendfor-trend=0.985). Paradoxically, the prevalence of ADR declined from 86.6% in 2001 to 51.0% in 2017 (pfor-trendfor-trend Conclusions While ADR is declining since 2001, TDR has been increasing, reaching a value of 13.1% by the end of 2017. It is urgent to develop public health programs to monitor levels and patterns of TDR in newly diagnosed patients.

ACS Style

Marta Pingarilho; Victor F Pimentel; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea Pineda-Pena; Pieter Libin; Kristof Theys; M. Rosario Oliveira Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis. Increasing prevalence of HIV-1 Transmitted Drug Resistance in Portugal: implications for first line treatment recommendations. 2020, 1 .

AMA Style

Marta Pingarilho, Victor F Pimentel, Isabel Diogo, Sandra Fernandes, Mafalda Miranda, Andrea Pineda-Pena, Pieter Libin, Kristof Theys, M. Rosario Oliveira Martins, Anne-Mieke Vandamme, Ricardo Camacho, Perpétua Gomes, Ana Abecasis. Increasing prevalence of HIV-1 Transmitted Drug Resistance in Portugal: implications for first line treatment recommendations. . 2020; ():1.

Chicago/Turabian Style

Marta Pingarilho; Victor F Pimentel; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea Pineda-Pena; Pieter Libin; Kristof Theys; M. Rosario Oliveira Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis. 2020. "Increasing prevalence of HIV-1 Transmitted Drug Resistance in Portugal: implications for first line treatment recommendations." , no. : 1.

Journal article
Published: 28 February 2020 in Viruses
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Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.

ACS Style

Victor Pimentel; Marta Pingarilho; Daniela Alves; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea-Clemencia Pineda-Pena; Pieter Libin; M. Rosário O. Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis. Molecular Epidemiology of HIV-1 Infected Migrants Followed Up in Portugal: Trends between 2001–2017. Viruses 2020, 12, 268 .

AMA Style

Victor Pimentel, Marta Pingarilho, Daniela Alves, Isabel Diogo, Sandra Fernandes, Mafalda Miranda, Andrea-Clemencia Pineda-Pena, Pieter Libin, M. Rosário O. Martins, Anne-Mieke Vandamme, Ricardo Camacho, Perpétua Gomes, Ana Abecasis. Molecular Epidemiology of HIV-1 Infected Migrants Followed Up in Portugal: Trends between 2001–2017. Viruses. 2020; 12 (3):268.

Chicago/Turabian Style

Victor Pimentel; Marta Pingarilho; Daniela Alves; Isabel Diogo; Sandra Fernandes; Mafalda Miranda; Andrea-Clemencia Pineda-Pena; Pieter Libin; M. Rosário O. Martins; Anne-Mieke Vandamme; Ricardo Camacho; Perpétua Gomes; Ana Abecasis. 2020. "Molecular Epidemiology of HIV-1 Infected Migrants Followed Up in Portugal: Trends between 2001–2017." Viruses 12, no. 3: 268.

Conference paper
Published: 01 January 2020 in Communications in Computer and Information Science
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One of the cornerstones in combating the HIV pandemic is the ability to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. We first present a method to learn epidemiological parameters from phylogenetic trees, using approximate Bayesian computation (ABC). The epidemiological parameters learned as a result of applying ABC are subsequently used in epidemiological models that aim to simulate a specific epidemic. Secondly, we continue by describing the development of a tree statistic, rooted in coalescent theory, which we use to relate epidemiological parameters to a phylogenetic tree, by using the simulated epidemics. We show that the presented tree statistic enables differentiation of epidemiological parameters, while only relying on phylogenetic trees, thus enabling the construction of new methods to ascertain the epidemiological state of an HIV epidemic. By using genetic data to infer epidemic sizes, we expect to enhance our understanding of the portions of the infected population in which diagnosis rates are low.

ACS Style

Pieter Libin; Nassim Versbraegen; Ana Abecasis; Perpetua Gomes; Tom Lenaerts; Ann Nowé. Towards a Phylogenetic Measure to Quantify HIV Incidence. Communications in Computer and Information Science 2020, 34 -50.

AMA Style

Pieter Libin, Nassim Versbraegen, Ana Abecasis, Perpetua Gomes, Tom Lenaerts, Ann Nowé. Towards a Phylogenetic Measure to Quantify HIV Incidence. Communications in Computer and Information Science. 2020; ():34-50.

Chicago/Turabian Style

Pieter Libin; Nassim Versbraegen; Ana Abecasis; Perpetua Gomes; Tom Lenaerts; Ann Nowé. 2020. "Towards a Phylogenetic Measure to Quantify HIV Incidence." Communications in Computer and Information Science , no. : 34-50.

Research article
Published: 30 September 2019 in PLOS ONE
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Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines. Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses. In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001). TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes.

ACS Style

Andrea-Clemencia Pineda-Peña; Marta Pingarilho; Guangdi Li; Bram Vrancken; Pieter Libin; Perpétua Gomes; Ricardo Jorge Camacho; Kristof Theys; Ana Barroso Abecasis; on behalf of the Portuguese HIV-1 Resistance Study Group. Drivers of HIV-1 transmission: The Portuguese case. PLOS ONE 2019, 14, e0218226 .

AMA Style

Andrea-Clemencia Pineda-Peña, Marta Pingarilho, Guangdi Li, Bram Vrancken, Pieter Libin, Perpétua Gomes, Ricardo Jorge Camacho, Kristof Theys, Ana Barroso Abecasis, on behalf of the Portuguese HIV-1 Resistance Study Group. Drivers of HIV-1 transmission: The Portuguese case. PLOS ONE. 2019; 14 (9):e0218226.

Chicago/Turabian Style

Andrea-Clemencia Pineda-Peña; Marta Pingarilho; Guangdi Li; Bram Vrancken; Pieter Libin; Perpétua Gomes; Ricardo Jorge Camacho; Kristof Theys; Ana Barroso Abecasis; on behalf of the Portuguese HIV-1 Resistance Study Group. 2019. "Drivers of HIV-1 transmission: The Portuguese case." PLOS ONE 14, no. 9: e0218226.

Journal article
Published: 01 August 2019 in Antimicrobial Agents and Chemotherapy
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Viral pathogens causing global disease burdens are often characterized by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be difficult to capture, particularly for agents in experimental stages or that are recently approved or expanded into new patient populations.

ACS Style

Kristof Theys; Pieter J. K. Libin; Kristel Van Laethem; Ana B. Abecasis. An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors. Antimicrobial Agents and Chemotherapy 2019, 63, 1 .

AMA Style

Kristof Theys, Pieter J. K. Libin, Kristel Van Laethem, Ana B. Abecasis. An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors. Antimicrobial Agents and Chemotherapy. 2019; 63 (8):1.

Chicago/Turabian Style

Kristof Theys; Pieter J. K. Libin; Kristel Van Laethem; Ana B. Abecasis. 2019. "An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors." Antimicrobial Agents and Chemotherapy 63, no. 8: 1.

Original article
Published: 20 June 2019 in Evolutionary Applications
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Aedes‐borne arboviruses have spread globally with outbreaks of vast impact on human populations and health systems. The West African archipelago of Cape Verde had its first outbreak of Dengue in 2009, at the time the largest recorded in Africa, and was one of the few African countries affected by the Zika virus epidemic. Aedes aegypti was the mosquito vector involved in both outbreaks. We performed a phylogeographic and population genetics study of A. aegypti in Cape Verde in order to infer the geographic origin and evolutionary history of this mosquito. These results are discussed with respect to the implications for vector control and prevention of future outbreaks. Mosquitoes captured before and after the Dengue outbreak on the islands of Santiago, Brava and Fogo were analyzed with two mitochondrial genes COI and ND4, 14 microsatellite loci and five kdr mutations. Genetic variability was comparable to other African populations. Our results suggest that A. aegypti invaded Cape Verde at the beginning of the Holocene from West Africa. Given the historic importance of Cape Verde in the transatlantic trade of the 16th –17th centuries, a possible contribution to the genetic pool of the founding populations in the New World cannot be fully discarded. However, contemporary gene flow with the Americas is likely to be infrequent. No kdr mutations associated with pyrethroid resistance were detected. The implications for vector control and prevention of future outbreaks are discussed. This article is protected by copyright. All rights reserved.

ACS Style

Patrícia Salgueiro; Célia Serrano; Bruno Gomes; Joana Alves; Carla Sousa; Ana Abecasis; Joao Pinto. Phylogeography and invasion history of Aedes aegypti , the Dengue and Zika mosquito vector in Cape Verde islands (West Africa). Evolutionary Applications 2019, 12, 1797 -1811.

AMA Style

Patrícia Salgueiro, Célia Serrano, Bruno Gomes, Joana Alves, Carla Sousa, Ana Abecasis, Joao Pinto. Phylogeography and invasion history of Aedes aegypti , the Dengue and Zika mosquito vector in Cape Verde islands (West Africa). Evolutionary Applications. 2019; 12 (9):1797-1811.

Chicago/Turabian Style

Patrícia Salgueiro; Célia Serrano; Bruno Gomes; Joana Alves; Carla Sousa; Ana Abecasis; Joao Pinto. 2019. "Phylogeography and invasion history of Aedes aegypti , the Dengue and Zika mosquito vector in Cape Verde islands (West Africa)." Evolutionary Applications 12, no. 9: 1797-1811.

Preprint
Published: 24 May 2019
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Viral pathogens causing global disease burdens are often characterised by high rates of evolutionary changes, facilitating escape from therapeutic or immune selective pressure. Extensive viral diversity at baseline can shorten the time to resistance emergence and alter mutational pathways, but the impact of genotypic background on the genetic barrier can be difficult to capture, in particular for antivirals in experimental stages, recently approved or expanded into new settings. We developed an evolutionary-based counting method to quantify the population genetic potential to resistance and assess differences between populations. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequences and corresponding knowledge gap on drug resistance. A large sequence dataset encompassing most prevailing subtypes and resistance mutations of first- and second-generation inhibitors were investigated. A varying genetic potential for resistance across HIV-1 subtypes was detected for 15 mutations at 12 positions, with notably 140S in subtype B, while 140C was discarded to vary across subtypes. An additional analysis for HIV-1 reverse transcriptase inhibitors identified a higher potential for 65R in subtype C, on the basis of a differential codon usage not reported before. The evolutionary interpretation of genomic differences for antiviral treatment remains challenging. Our framework advances existing counting methods with an increased sensitivity that identified novel subtype dependencies as well as rejected previous statements. Future applications include novel HIV-1 drug classes as well as other viral pathogens.

ACS Style

Kristof Theys; Pieter Libin; Kristel Van Laethem; Ana B Abecasis. An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors. 2019, 647297 .

AMA Style

Kristof Theys, Pieter Libin, Kristel Van Laethem, Ana B Abecasis. An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors. . 2019; ():647297.

Chicago/Turabian Style

Kristof Theys; Pieter Libin; Kristel Van Laethem; Ana B Abecasis. 2019. "An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors." , no. : 647297.

Journal article
Published: 10 May 2019 in Scientific Reports
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HIV-1 subtypes associate with differences in transmission and disease progression. Thus, the existence of geographic hotspots of subtype diversity deepens the complexity of HIV-1/AIDS control. The already high subtype diversity in Portugal seems to be increasing due to infections with sub-subtype A1 virus. We performed phylogenetic analysis of 65 A1 sequences newly obtained from 14 Portuguese hospitals and 425 closely related database sequences. 80% of the A1 Portuguese isolates gathered in a main phylogenetic clade (MA1). Six transmission clusters were identified in MA1, encompassing isolates from Portugal, Spain, France, and United Kingdom. The most common transmission route identified was men who have sex with men. The origin of the MA1 was linked to Greece, with the first introduction to Portugal dating back to 1996 (95% HPD: 1993.6–1999.2). Individuals infected with MA1 virus revealed lower viral loads and higher CD4+ T-cell counts in comparison with those infected by subtype B. The expanding A1 clusters in Portugal are connected to other European countries and share a recent common ancestor with the Greek A1 outbreak. The recent expansion of this HIV-1 subtype might be related to a slower disease progression leading to a population level delay in its diagnostic.

ACS Style

Pedro M. M. Araújo; BEST-HOPE study group; Alexandre Carvalho; Marta Pingarilho; Ana Abecasis; Nuno S. Osório. Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries. Scientific Reports 2019, 9, 1 -10.

AMA Style

Pedro M. M. Araújo, BEST-HOPE study group, Alexandre Carvalho, Marta Pingarilho, Ana Abecasis, Nuno S. Osório. Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries. Scientific Reports. 2019; 9 (1):1-10.

Chicago/Turabian Style

Pedro M. M. Araújo; BEST-HOPE study group; Alexandre Carvalho; Marta Pingarilho; Ana Abecasis; Nuno S. Osório. 2019. "Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries." Scientific Reports 9, no. 1: 1-10.

Evaluation study
Published: 08 May 2019 in PLOS Neglected Tropical Diseases
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In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.

ACS Style

Vagner Fonseca; Pieter J. K. Libin; Kristof Theys; Nuno R. Faria; Marcio R. T. Nunes; Maria I. Restovic; Murilo Freire; Marta Giovanetti; Lize Cuypers; Ann Nowe; Ana Abecasis; Koen Deforche; Gilberto A. Santiago; Isadora de Siqueira; Emmanuel J. San; Kaliane C. B. Machado; Vasco Azevedo; Ana Maria Bispo-De Filippis; Rivaldo Venâncio Da Cunha; Oliver Pybus; Anne-Mieke Vandamme; Luiz Alcantara; Tulio De Oliveira. A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLOS Neglected Tropical Diseases 2019, 13, e0007231 .

AMA Style

Vagner Fonseca, Pieter J. K. Libin, Kristof Theys, Nuno R. Faria, Marcio R. T. Nunes, Maria I. Restovic, Murilo Freire, Marta Giovanetti, Lize Cuypers, Ann Nowe, Ana Abecasis, Koen Deforche, Gilberto A. Santiago, Isadora de Siqueira, Emmanuel J. San, Kaliane C. B. Machado, Vasco Azevedo, Ana Maria Bispo-De Filippis, Rivaldo Venâncio Da Cunha, Oliver Pybus, Anne-Mieke Vandamme, Luiz Alcantara, Tulio De Oliveira. A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLOS Neglected Tropical Diseases. 2019; 13 (5):e0007231.

Chicago/Turabian Style

Vagner Fonseca; Pieter J. K. Libin; Kristof Theys; Nuno R. Faria; Marcio R. T. Nunes; Maria I. Restovic; Murilo Freire; Marta Giovanetti; Lize Cuypers; Ann Nowe; Ana Abecasis; Koen Deforche; Gilberto A. Santiago; Isadora de Siqueira; Emmanuel J. San; Kaliane C. B. Machado; Vasco Azevedo; Ana Maria Bispo-De Filippis; Rivaldo Venâncio Da Cunha; Oliver Pybus; Anne-Mieke Vandamme; Luiz Alcantara; Tulio De Oliveira. 2019. "A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes." PLOS Neglected Tropical Diseases 13, no. 5: e0007231.

Journal article
Published: 03 May 2019 in Ticks and Tick-borne Diseases
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The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the continental territory and the islands of São Miguel, in the Azores, and Madeira), as well as in the Spanish western regions of Extremadura and Castilla and León. Phlebovirus sequences were frequently detected (L-segment) from both questing and feeding ticks, but especially in Rhipicephalus sanguineus sensu lato (s.l.) specimens. These sequences were detected in adult ticks, as well as nymphs and eggs, supporting the hypothesis of viral maintenance by vertical transmission. Though multiple genetic groups could be identified in phylogenetic trees (AnLuc, KarMa, RiPar virus 1, and Spanish group 1 and 2), all the sequences from Portugal and Spain shared common ancestry with other viral sequence obtained from samples collected over a large geographic coverage. Spatiotemporal analysis placed Middle-East as the geographic origin of the most recent common ancestor (MRCA) of all phleboviruses analysed in the present study. More recent viral transitions might include migrations from Spain to continental Portugal, and from there to the Portuguese Islands. Our findings suggest that the time of the MRCA of phleboviruses was dated around 225 years ago [95% HPD: 124-387 year before the last sampling date].

ACS Style

Victor Pimentel; Rita Afonso; Mónica Nunes; Maria Luisa Vieira; Daniel Bravo-Barriga; Eva Frontera; Manuel Martinez; André Pereira; Carla Maia; Maria Das Neves Paiva-Cardoso; Ferdinando Bernardino Freitas; Ana B. Abecasis; Ricardo Parreira. Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences. Ticks and Tick-borne Diseases 2019, 10, 942 -948.

AMA Style

Victor Pimentel, Rita Afonso, Mónica Nunes, Maria Luisa Vieira, Daniel Bravo-Barriga, Eva Frontera, Manuel Martinez, André Pereira, Carla Maia, Maria Das Neves Paiva-Cardoso, Ferdinando Bernardino Freitas, Ana B. Abecasis, Ricardo Parreira. Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences. Ticks and Tick-borne Diseases. 2019; 10 (4):942-948.

Chicago/Turabian Style

Victor Pimentel; Rita Afonso; Mónica Nunes; Maria Luisa Vieira; Daniel Bravo-Barriga; Eva Frontera; Manuel Martinez; André Pereira; Carla Maia; Maria Das Neves Paiva-Cardoso; Ferdinando Bernardino Freitas; Ana B. Abecasis; Ricardo Parreira. 2019. "Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences." Ticks and Tick-borne Diseases 10, no. 4: 942-948.

Journal article
Published: 18 April 2019 in BMC Health Services Research
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Tuberculosis (TB) is still a major global health problem. The increasing number of cases observed among foreign-born populations contrasts with the decreasing trends observed in later years in some high-income countries. Healthcare providers are key interveners in the control of TB and HIV-TB infections. In this study, we aimed to explore the perspectives of healthcare providers working in primary care in Portugal about the provision of TB care for migrant patients with TB or HIV-TB co-infection. We applied a mixed-methods approach using an online survey and semi-structured interviews with primary healthcare providers. A total of 120 Portuguese healthcare providers participated in the survey, and 17 were interviewed. Survey and interview data were analysed applying descriptive statistics and thematic analysis, respectively. Migrants' lack of knowledge on TB disease and its symptoms was the main reason for advanced-stage presentation of cases. Their high mobility and social isolation affect adherence to treatment. The providers also listed several barriers to migrants' access and use of TB care. The most frequently referred were limited socioeconomic resources, complex bureaucracy at the point of access and registration for healthcare services, especially for undocumented migrants, and obstacles for social protection. Providers also advocated more training initiatives on migrants' health, social and cultural contexts, on HIV and TB integrated care, and on TB scientific update for general practitioners and nurses working at primary healthcare centres. Future efforts should provide measures to overcome social, economic and administrative obstacles to care for TB-infected migrants, and promote regular training initiatives for national healthcare providers in order to raise awareness and facilitate better care to culturally diverse populations with TB.

ACS Style

Ana Maria Tavares; Ana Cristina Garcia; Ana Gama; Ana B. Abecasis; Miguel Viveiros; Sónia Dias. Tuberculosis care for migrant patients in Portugal: a mixed methods study with primary healthcare providers. BMC Health Services Research 2019, 19, 233 .

AMA Style

Ana Maria Tavares, Ana Cristina Garcia, Ana Gama, Ana B. Abecasis, Miguel Viveiros, Sónia Dias. Tuberculosis care for migrant patients in Portugal: a mixed methods study with primary healthcare providers. BMC Health Services Research. 2019; 19 (1):233.

Chicago/Turabian Style

Ana Maria Tavares; Ana Cristina Garcia; Ana Gama; Ana B. Abecasis; Miguel Viveiros; Sónia Dias. 2019. "Tuberculosis care for migrant patients in Portugal: a mixed methods study with primary healthcare providers." BMC Health Services Research 19, no. 1: 233.

Journal article
Published: 26 February 2019 in Journal of Infectious Diseases
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Background Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. Methods Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. Results We identified 5 subtype B Portuguese clades (26–79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998–2000) and 2000 (95% BCI, 1998–2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73–2.09) to 0.62 (95% BCI,.52–.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39–1.59) to 0.72 (95% BCI, .63–.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. Conclusions The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.

ACS Style

Tetyana I Vasylyeva; Louis Du Plessis; Andrea C Pineda-Peña; Denise Kühnert; Philippe Lemey; Anne-Mieke Vandamme; Perpetua Gomes; Ricardo J Camacho; Oliver Pybus; Ana Abecasis; Nuno R Faria. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. Journal of Infectious Diseases 2019, 220, 233 -243.

AMA Style

Tetyana I Vasylyeva, Louis Du Plessis, Andrea C Pineda-Peña, Denise Kühnert, Philippe Lemey, Anne-Mieke Vandamme, Perpetua Gomes, Ricardo J Camacho, Oliver Pybus, Ana Abecasis, Nuno R Faria. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. Journal of Infectious Diseases. 2019; 220 (2):233-243.

Chicago/Turabian Style

Tetyana I Vasylyeva; Louis Du Plessis; Andrea C Pineda-Peña; Denise Kühnert; Philippe Lemey; Anne-Mieke Vandamme; Perpetua Gomes; Ricardo J Camacho; Oliver Pybus; Ana Abecasis; Nuno R Faria. 2019. "Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology." Journal of Infectious Diseases 220, no. 2: 233-243.

Journal article
Published: 08 October 2018 in Bioinformatics
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Supplementary data is available at Bioinformatics online.

ACS Style

Pieter J K Libin; Koen Deforche; Ana Abecasis; Kristof Theys. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. Bioinformatics 2018, 35, 1763 -1765.

AMA Style

Pieter J K Libin, Koen Deforche, Ana Abecasis, Kristof Theys. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. Bioinformatics. 2018; 35 (10):1763-1765.

Chicago/Turabian Style

Pieter J K Libin; Koen Deforche; Ana Abecasis; Kristof Theys. 2018. "VIRULIGN: fast codon-correct alignment and annotation of viral genomes." Bioinformatics 35, no. 10: 1763-1765.

Journal article
Published: 01 October 2018 in AIDS Research and Human Retroviruses
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Objectives: A 4 years old child born to an HIV-1 seronegative mother was diagnosed with HIV-1, the main risk factor being transmission from the child’s father who was seroconverting at the time of the child’s birth. In the context of a forensic investigation, we aimed to identify the source of infection of the child and date the transmission event. Methods: Samples were collected from the father and child at two time points about 4 years after the child’s birth. Partial segments of three HIV-1 genes (gag, pol, and env) were sequenced and maximum likelihood (ML) and Bayesian methods were used to determine direction and estimate date of transmission. Neutralizing antibodies were determined using a single cycle assay. Results: Bayesian trees displayed a paraphyletic-monophyletic topology in all three genomic regions, with the father’s host-label at the root which is consistent with father-to-son transmission. ML trees found similar topologies in gag and pol and a monophyletic-monophyletic topology in env. Analysis of the time of the most recent common ancestor of each HIV-1 gene population indicated that the child was infected shortly after the father. Consistent with the infection history, both father and son developed broad and potent HIV-specific neutralizing antibody responses. Conclusions: The direction of transmission implicated the father as the source of transmission. Transmission occurred during the seroconversion period when the father was unaware of the infection and was likely accidental. This case shows how genetic, phylogenetic, and serological data can contribute for the forensic investigation of HIV transmission.

ACS Style

Ifeanyi Ezeonwumelu; Inês Bártolo; Francisco Martin; Ana B Abecasis; Teresa Campos; Ethan O. Romero-Severson; Thomas Leitner; Nuno Taveira. Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period. AIDS Research and Human Retroviruses 2018, 34, 857 -862.

AMA Style

Ifeanyi Ezeonwumelu, Inês Bártolo, Francisco Martin, Ana B Abecasis, Teresa Campos, Ethan O. Romero-Severson, Thomas Leitner, Nuno Taveira. Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period. AIDS Research and Human Retroviruses. 2018; 34 (10):857-862.

Chicago/Turabian Style

Ifeanyi Ezeonwumelu; Inês Bártolo; Francisco Martin; Ana B Abecasis; Teresa Campos; Ethan O. Romero-Severson; Thomas Leitner; Nuno Taveira. 2018. "Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period." AIDS Research and Human Retroviruses 34, no. 10: 857-862.

Preprint
Published: 06 September 2018
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Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit for these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codoncorrect alignments of large datasets, with standardized genome annotation and various alignment export formats.VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project.

ACS Style

Pieter Libin; Koen Deforche; Ana B. Abecasis; Kristof Theys. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. 2018, 409052 .

AMA Style

Pieter Libin, Koen Deforche, Ana B. Abecasis, Kristof Theys. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. . 2018; ():409052.

Chicago/Turabian Style

Pieter Libin; Koen Deforche; Ana B. Abecasis; Kristof Theys. 2018. "VIRULIGN: fast codon-correct alignment and annotation of viral genomes." , no. : 409052.